| Hilfe-Text | The program structure is a free software package for using multi-locus
genotype data to investigate population structure. Its uses include
inferring the presence of distinct populations, assigning individuals
to populations, studying hybrid zones, identifying migrants and admixed
individuals, and estimating population allele frequencies in situations
where many individuals are migrants or admixed. It can be applied to
most of the commonly-used genetic markers, including SNPS,
microsatellites, RFLPs and AFLPs.
In order to simplify batch runs and make it easier to run simulations
involving structure, the run-time version of Structure has added
command-line flags that update the values of certain parameters,
over-riding the values set in 'mainparams'.
These are as follows:
-m (mainparams) Read a different parameter input file instead of
mainparams
-e (extraparams) Read a different parameter input file instead of
extraparams
-s (stratparams) Read a different parameter input file instead of
stratparams. (For use with the accompanying program, STRAT,
for association mapping.)
-K (MAXPOPS) Change the number of populations.
-L (NUMLOCI) Change the number of loci.
-N (NUMINDS) Change the number of individuals.
-i (input file) Read data from a different input file.
-o (output file) Print results to a different output file.
-D (SEED) Initialize the random number generation using the value SEED.
Note that RANDOMIZE MUST be set to 0 to use this option.)
Thus, to override one of the preset parameter values, we invoke structure
and then use the relevant flag, followed by the new parameter value.
The flag and new value are separated by a space. The flags can be used
in any order.
For example, to change the number of assumed populations to 5, and
direct the output to a file called output5, we could call structure
as follows: ./structure -K 5 -o output5
More documentation:
* http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/structure_doc.pdf
/opt/bwhpc/common/bio/structure/2.3.4/console/structure_doc.pdf
In case of problems, please contact: bwhpc (at) uni-konstanz.de
*** THIS IS THE COMMAND-LINE version ***
ATTENTION: We need at least a 'mainparams' and 'extraparams'-file
in your current directory to get 'structure' started.
Examples are found in:
/opt/bwhpc/common/bio/structure/2.3.4/console/mainparams
/opt/bwhpc/common/bio/structure/2.3.4/console/extraparams
/opt/bwhpc/common/bio/structure/2.3.4/bwhpc-examples/*
and READ CAREFULLY!
/opt/bwhpc/common/bio/structure/2.3.4/bwhpc-examples/README.bwhpc
This module is available for all users. |